ZMB Member Daniel Hoffmann
ZMB Member
Daniel Hoffmann
Next ZMB-Member
Prof. Dr. Daniel Hoffmann
Faculty of Biology
University of Duisburg-Essen
Universitätsstr. 2
45141 Essen
- +49 201 183 4391
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- Selected Publications
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- ZMB Research Program
Molecular and Chemical Cell Biology
Research Overview
Quantitative Biology
Biology is a messy science. Its subjects - biomolecules, cells, tissues, organisms, ecosystems, etc. - are highly complex and variable. This makes it difficult to pin down laws as reliably as, say, in physics. It is therefore not surprising that biologists are fully occupied with taming their complex subjects, and with obtaining (using a minimum of mathematics) simple, qualitative results from experiments.
However, we know that living systems are essentially quantitative; e.g. it matters a lot whether you have too little or too much of a substance in an organism. If we want to account for this, we have to use quantitative mathematical and computational models of biological systems or biological data. This is exactly what we do.
In our research we are developing mathematical or computational models for biological systems. Often these models are probabilistic because biological systems are variable and not completely characterized, and probabilities are an effective way of dealing with variability. We can then infer quantitative relationships by computational methods such as Bayesian analyses.
This is a Swiss knife approach that is basically applicable to all kinds of biology. Accordingly, we have fruitful collaborations with researchers from many areas, e.g. developmental biologists, virologists, immunologists, cancer researchers, or ecologists.
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Selected Publications
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HBV shows different levels of adaptation to HLA class I-associated selection pressure correlating with markers of replicationIn: Journal of Hepatology (2024) in pressOnline Full Text: dx.doi.org/ (Open Access)
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HAMdetector : A Bayesian regression model that integrates information to detect HLA-associated mutationsIn: Bioinformatics Vol. 38 (2022) Nr. 9, pp. 2428 - 2436Online Full Text: dx.doi.org/; Online Full Text: dx.doi.org/ (Open Access)
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Specific inhibition of the Survivin–CRM1 interaction by peptide-modified molecular tweezersIn: Nature Communications Vol. 12 (2021) Nr. 1, pp. 1505Online Full Text: dx.doi.org/ Online Full Text (Open Access)
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IgGeneUsage : differential gene usage in immune repertoiresIn: Bioinformatics Vol. 36 (2020) Nr. 11, pp. 3590 - 3591Online Full Text: dx.doi.org/
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A network of trans-cortical capillaries as mainstay for blood circulation in long bonesIn: Nature Metabolism Vol. 1 (2019) Nr. 2, pp. 236 - 250Online Full Text: dx.doi.org/ Online Full Text (Open Access)
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Mutations in Hepatitis D Virus Allow It to Escape Detection by CD8⁺ T Cells and Evolve at the Population LevelIn: Gastroenterology Vol. 156 (2019) Nr. 6, pp. 1820 - 1833Online Full Text: dx.doi.org/ (Open Access)
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Viral escape contributes to the failure of hepatitis D virus-specific CD8+ T-cells and drives evolution of HDVIn: Journal of Hepatology Vol. 70 (2019) Nr. Suppl. 1, pp. e21Online Full Text: dx.doi.org/
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Biased IGH VDJ gene repertoire and clonal expansions in B cells of chronically hepatitis C virus–infected individualsIn: Blood Vol. 131 (2018) Nr. 5, pp. 546 - 557Online Full Text: dx.doi.org/ (Open Access)
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Adaptation of the Hepatitis B Virus Core Protein to CD8+ T-Cell Selection PressureIn: Hepatology Vol. 62 (2015) Nr. 1, pp. 47 - 56Online Full Text: dx.doi.org/ (Open Access)
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HLA-B*27 is protective against HCV genotype 1 and 3 and associated with targeting of distinct genotype-specific CD8(+) cell epitopesIn: Journal of Hepatology Vol. 60 (2014) Nr. Suppl. 1, pp. 140Online Full Text: dx.doi.org/
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Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptidesIn: Nature Communications Vol. 2 (2011) pp. 453Online Full Text: dx.doi.org/ (Open Access)
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CD8+ T-Cell Response Promotes Evolution of Hepatitis C Virus Nonstructural ProteinsIn: Gastroenterology Vol. 140 (2011) Nr. 7, pp. 2064 - 2073Online Full Text: dx.doi.org/
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Computational methods for the design of effective therapies against drug resistant HIV strainsIn: Bioinformatics Vol. 21 (2005) Nr. 21, pp. 3943 - 3950Online Full Text: dx.doi.org/ (Open Access)
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Mtreemix : A software package for learning and using mixture models of mutagenetic treesIn: Bioinformatics Vol. 21 (2005) Nr. 9, pp. 2106 - 2107Online Full Text: dx.doi.org/ (Open Access)
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Methods for optimizing antiviral combination therapiesIn: Bioinformatics Vol. 19 (2003) Nr. Suppl 1, pp. i16 - i25Online Full Text: dx.doi.org/ (Open Access)
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Web Site : The Protein Information ResourceIn: Angewandte Chemie International Edition Vol. 41 (2002) Nr. 6, pp. 1075 - 1075Online Full Text: dx.doi.org/
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Strain-Induced “Band Flips” in Cyclodecaamylose and Higher HomologuesIn: Angewandte Chemie International Edition Vol. 37 (1998) Nr. 5,Online Full Text: dx.doi.org/
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Structures of the Common Cyclodextrins and Their Larger Analogues -- Beyond the DoughnuIn: Chemical Reviews Vol. 98 (1998) pp. 1787 - 1802
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Structures of the common cyclodextrins and their larger analogues : beyond the doughnutIn: Chemical Reviews Vol. 98 (1998) Nr. 5, pp. 1787 - 1802Online Full Text: dx.doi.org/